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User Guide to Protean 3D — 17.2

18.0

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User Guide to Protean 3D — 17.2
- User Guide to Protean 3D — 18.0

Welcome to Protean 3D
- Separately-licensed services that integrate with Protean 3D
Protean 3D Tutorials
Protean 3D Interface
- Welcome screen
- Project tabs
- Protean 3D toolbar
- Views
- Panels
- Motion Library
  - Try it! – Open a multi-model file from the Motion Library
Customize the Look and Layout
- Customize the appearance and layout of views
- Customize the layout of other window components
- Save the layout and apply it to other projects
Open a File or Project
- Open one or more local files
  - Change the default application for opening files
- Type or paste a protein sequence
- Open a PDB file when you know the ID
- Open a PDB file when you don’t know the ID
- Open a structure from the Motion Library
- Open an existing Protean 3D project
Search for Sequences Online
- Search for sequence matches (BLAST)
- Search for text or accession number matches (Entrez)
Align Multiple Structures
- Try it! – Align multiple structures using jFATCAT
Make a Selection
- Try it! – Make a selection from the Sequence view
Work with Features
Overlay One Structure on Another
Create or Find Variants using Protein Design
- Protein Design wizard: Workflow
- Protein Design wizard: Structure
- Protein Design wizard: Substitutes
- Protein Design wizard: Options
- Protein Design wizard: Job
- View progress and see variant results
- Use Protein Design for site-directed mutagenesis
- Select neighboring residues
Evaluate Variants Produced in a SeqMan NGen Assembly
- Part A: Create a templated assembly in SeqMan NGen
- Part B (optional): Filter for variants of interest in ArrayStar
- Part C: View variants in SeqMan Pro
- Part D: View the protein structure in Protean 3D
NovaFold: protein structure prediction
- Run NovaFold through Protean 3D
- Run Nova applications through the DNASTAR website
- Run Nova applications locally
NovaFold Antibody: antibody interaction prediction
- Run NovaFold Antibody through Protean 3D
NovaDock: protein-protein docking
- Run NovaDock through Protean 3D
- Try it! – Phage display assembly, translation and prediction
Save and Export
- Save a document
- Export a still image
- Export a structure file
- Export an animation or video
- Export data from the Text, Table or Pairwise views
- Export a table of results from the Analysis view
- Save or export a report
Close and Exit
Miscellaneous Tasks
- Use basic editing commands
- Set preferences
- Synchronize sequence updates between two Lasergene applications
- Turn off usage logging
- Use a mouse or trackpad with Protean 3D
- Change the default print size
- Prevent firewall issues when downloading from the Motion Library
- Troubleshoot the error “A different version is running”
- Troubleshoot blank Protean 3D window on Parallels Desktop
Appendix
- Glossary
- Supported file types
- IUPAC codes
- Installed Lasergene file locations
- Useful links
- Research references
- Acknowledgements

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Acknowledgements

DNASTAR thanks the authors for the PDB structure files used in our written tutorials:

Research references

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